This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.
Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Cmd+Shift+Enter.
#### Install morpheus
# devtools::install_github('cmap/morpheus.R')
# Load morpheus
library(morpheus)
library(datasets)
data(mtcars)
head(mtcars)# mpg cyl disp hp drat wt qsec vs am gear carb
# Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
# Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
# Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
# Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
# Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
# Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
morpheus(mtcars)
### cluster by correlation
### scalingMode = "fixed" makes it so that it doesn't automatically rescale colors by rows
# morpheus( mtcars,
# distfun = function(x) as.dist(1 - cor(t(x), use = "pairwise.complete.obs")),
# Rowv = T,
# Colv = T,
# dendrogram = "both",
# colorScheme = list(scalingMode = "fixed",
# colors = list("blue", "white", "red"))
# )
#### example of shiny code
# output$myheatmap = renderMorpheus({
# morpheus( mtcars,
# distfun = function(x) as.dist(1 - cor(t(x), use = "pairwise.complete.obs")),
# Rowv = T,
# Colv = T,
# dendrogram = "both",
# colorScheme = list(scalingMode = "fixed", values = list(0,50,100),
# colors = list("blue", "white", "red") )
# )
# })
#
# morpheusOutput("myheatmap", height = "800px")Add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Cmd+Option+I.
When you save the notebook, an HTML file containing the code and output will be saved alongside it (click the Preview button or press Cmd+Shift+K to preview the HTML file).
The preview shows you a rendered HTML copy of the contents of the editor. Consequently, unlike Knit, Preview does not run any R code chunks. Instead, the output of the chunk when it was last run in the editor is displayed.